Nucleic Acids With Metal‐Mediated Base Pairs and Their Applications

Abstract

Metal‐mediated base pairs represent an elegant way for the site‐specific functionalisation of nucleic acids. In this type of base pair, the hydrogen bonds between complementary nucleobases are replaced formally by coordinative bonds to one or more transition‐metal ions. This Review presents an overview of metal‐mediated base pairs reported so far. It gives an insight into the characterisation of metal‐mediated base pairs and into the structures of the resulting metal‐modified nucleic acids. In addition, a summary of applications exploiting the formation of metal‐mediated base pairs is presented. The applications include, for example, metal‐ion sensors of various types, a protein sensor, and DNA‐based molecular machines. Initial reports on the potential use of metal‐mediated base pairs in the context of charge transfer through nucleic acid double helices are summarised as well.

Artificial DNA Base Pairing Mediated by Diverse Metal Ions

“…Such large increases in T m are an important prerequisite for the use of a metalmediated base pair in a sensor application. 18 7-Deazaadenine derivatives are components of the latest addition to the class of Ag(I)-mediated base pairs. In the 7D A Ag I T base pair (Figure 4d), the Ag + ion is proposed to formally replace the hydrogen atom in one of the two Watson Crick-type hydrogen bonds typically found in a canonical AT base pair.…”

“…As already mentioned, Hg(II)-mediated thymine base pairing (THg II T) has been well investigated and extensively applied in the fields of DNA-based material sciences and DNA nanotechnology. 18,19 The association constant K a for an Hg 2+ binding to a DNA duplex containing one TT mispair, forming a THg II T pair, was estimated to be 5 © 10 5 M ¹1 . 51 The K a value indicates a thermodynamic stability similar to the CAg…”

“…More recently, the versatility of the THg II T base pair has attracted much attention in this field. 18,19 In a manner similar to the thymine base, a cytosine nucleobase (C) forms an Ag(I)-mediated base pair, CAg I C (Figure 2b). 22 Due to the facile preparation of natural DNA strands, these metal-mediated base pairs are now extensively studied and applied to DNA nanotechnology and DNA supramolecular chemistry.…”

DNA-bound metal ions: recent developments

“…In addition to forming base pairs between naturally occurring bases, metallo-base pairing using synthetic ligands that behave like nucleobases allows base pairing that is orthogonal to naturally occurring base pairs, opening opportunities to expand genetic information and information storage capabilities. Metal-mediated base pairing involving naturally occurring bases and synthetic nucleobases is a rapidly expanding area for which several reviews exist (73)(74)(75)(76).…”

A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs

“…[2] Their site-specific functionalization can be achieved by introducing metal ions at pre-defined positions via the formation of metal-mediated base pairs. [3][4][5][6][7][8][9] In these base pairs, the hydrogen bonds between complementary nucleobases are formally replaced by coordinative bonds to a metal ion located between the nucleobases. While the naturally occurring pyrimidine nucleosides cytidine and thymidine are known to be capable of forming silver(I)-and mercury(II)-mediated base pairs, respectively, numerous artificial nucleosides have been developed for an application in metal-mediated base pairs.…”